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prepare drude initial coordinates
#38144 01/07/21 10:44 AM
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Hello,

I have coordinates of 32 glucose molecules that forms eight unit cells of a certain point group of a crystal. There are no bonds between glucose molecules. If I want to prepare the drude system, how could I load the pdb without splitting them. I tried the following:
read sequ aglc 32
open read card name "input.pdb" unit 21
generate A first none last none setup warn drude dmass 0.4
autogenerate angles dihedrals
read coor pdb unit 21
coor sdrude
coor shake

Error message shows: After reading, there are no coordinates for selected atom
If I have to read each molecule separately, how could I avoid splitting the pdb into 32 pieces?
Or do I have to rebuild the crystal from one asymmetric unit?
Either is very inconvenient for me

Last edited by Allen_123; 01/07/21 11:15 AM.
Re: prepare drude initial coordinates
Allen_123 #38145 01/07/21 06:12 PM
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rmv Online Content
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PDB is not a native CHARMM format, and there are a number of variations in the PDB format produced by different programs which can make import challenging at times.

I suggest using the UNIVersal I/O specification, as outlined in the second example in this post which reads a complex PDB file in a single pass.


Rick Venable
computational chemist


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